Regarding the NYFD regulation of Amtrak versus the pollution regulation of airliners: This is often falling under constitutional law, which is the most nuanced and long-winded discussion ever. I didn't get the best grades in that class to say the least. It's a specialty for very bright people.
Essentially constitutional law is the law of laws. Part of that is the process of making and applying laws, and a subset of that is figuring out which jurisdiction laws apply - federal, state, or local, and who prevails. As an oversimplification, what ever is not specifically reserved for the feds is fair game for state/local.
Because of that, a local jurisdiction can have harder laws than a bigger jurisdiction. A famous example is that of OSHA. There is federal OSHA setting safety rules, but then certain states are well known for more restrictive safety rules - Michigan, California, Washington are the three most famous.
You also have air pollution rules, and California is know for having more restrictive car emission standards. For decades automakers made special models for California that were essentially the same thing, but the timing was dialed back a bit and the cats were more restrictive, the thinking being that less power and more filter produced less emissions and used less gas.
In the case of regulating the Park Avenue tunnel, it appears the regulations are more restrictive safety standards that probably have a lot of merit. Park Avenue tunnel has seen accidents and fires. The steamers that started it all, and then the Jets and FL9's that did indeed catch fire.
Where local over-regulation crosses the line is when it restricts interstate commerce, because the commerce clause of the US constitution specifically reserves the ability for the feds to regulate interstate commerce.
The best example I can think of is when Arizona mandated five-man crews after SP went down to two or three man. Freights would have to stop just inside Arizona, pick up flagmen, then drop them off on the other end of the state. SP sued the state saying that restricts interstate commerce, and that the state could not do that. SP won.
Comparing that to our NYC tunnel issue, they would probably have to prove that special fuel tanks or escape hatches somehow restrict commerce, and that said commerce is interstate. Amtrak has maintained roughly the same schedule as New York Central (or increased it) circa 1967, so it's hard to make a case for interference. Also, very few diesel or dual mode trains originating at NYP leave the state, so it's not interstate anyway.
In the end, it's a moot point anyway. Most of the diesel or dual mode trains leaving NYP and going through tunnels are demanded by and funded by New York State anyway.
The new Acela: It's not Aveliable.
